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Stable Isotope Probing of Microorganisms in Environmental Samples with H218O

  • Egbert SchwartzEmail author
  • Michaela Hayer
  • Bruce A. Hungate
  • Rebecca L. Mau
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)

Abstract

We describe a protocol for investigating microbial growth in environmental samples via stable isotope probing (SIP) with H218O. Water is a universal substrate for all microorganisms and replication is required for DNA to become labeled with 18O. By measuring how much the DNA of each taxon becomes enriched with 18O when an environmental sample is incubated with H218O, it is feasible to quantify that population’s DNA replication rate, which is a proxy for growth.

Key words

Stable isotope probing H218Microbial growth 

Notes

Acknowledgments

This research was supported by the National Science Foundation (NSF DEB-1241094) and the Department of Energy’s Biological Systems Science Division, Program in Genomic Science (DE-SC0010579 and DE-SC0016207).

References

  1. 1.
    Blake RE, Alt JC, Martini AM (2001) Oxygen isotope ratios of PO4: an inorganic indicator of enzymatic activity and P metabolism and a new biomarker in the search for life. Proc Natl Acad Sci U S A 98:2148–2153CrossRefGoogle Scholar
  2. 2.
    Richards OC, Boyer PD (1966) 18O labeling of deoxyribonucleic acid during synthesis and stability of label during replication. J Mol Biol 19:109–119CrossRefGoogle Scholar
  3. 3.
    Schwartz E (2007) Characterization of growing microorganisms in soil by stable isotope probing with H218O. Appl Environ Microbiol 73:2541–2546CrossRefGoogle Scholar
  4. 4.
    Koch BJ, McHugh TA, Hayer M, Schwartz E, Blazewicz SJ, Dijkstra P et al (2018) Estimating taxon-specific population dynamics in diverse microbial communities. Ecosphere 9:e02090CrossRefGoogle Scholar
  5. 5.
    Schwartz E, Hayer M, Hungate BA, Koch B, McHugh TA, Mercurio W et al (2016) Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples. Curr Opin Biotechnol 41:14–18CrossRefGoogle Scholar
  6. 6.
    Blazewicz SJ, Schwartz E, Firestone MK (2014) Growth and mortality of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil. Ecology 95:1162–1172CrossRefGoogle Scholar
  7. 7.
    Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N et al (2015) Quantitative microbial ecology through stable isotope probing. Appl Environ Microbiol 81:7570–7581CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Egbert Schwartz
    • 1
    Email author
  • Michaela Hayer
    • 1
  • Bruce A. Hungate
    • 1
  • Rebecca L. Mau
    • 1
    • 2
  1. 1.Department of Biological Sciences, Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffUSA
  2. 2.Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffUSA

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